New ways to observe and manipulate cellular function have revolutionized our understanding of biology. Such methods have undergone multiple paradigm shifts in history, from Hooke's microscope and Cajal's staining of neurons, to modern fluorescent imaging based on green fluorescent protein (GFP) and opsin-based optogenetics. These modern genetically encoded methods, defined by their use of protein-based agents that can be expressed by cells, provide key capabilities such as cell-specific targeted expression, continued production in dividing cells, and coupling with state-of-the-art genetic engineering methods. However, as most of these protein tools rely on optical interactions, they are fundamentally limited by the ~ 1 mm penetration depth of light into opaque tissue. As the objects of study increase in size from cell cultures and translucent organisms such as C. elegans, via small rodents, to human beings, this limitation becomes increasingly severe. To overcome this technological challenge, I aim to develop next-generation methods that are both genetically encoded and able to communicate with deeply penetrant forms of energy. In particular, I will leverage the unique physical and biochemical properties of gas vesicles (GVs), a class of gas-filled protein- only nanostructures discovered in certain photosynthetic microbes. In Aim 1, a new method, ?sonomagnetic imaging? (SMI), will be developed, which takes advantage of GVs' dual ability to induce contrast for magnetic resonance imaging (MRI) and interact with ultrasound pulses for selective erasing of such contrast. In parallel, a new method to control gene expression, sonomechanical control (SMC), will be developed in Aim 2 wherein ultrasound pulses can collapse GVs and trigger signaling pathways to activate gene expression at high spatial precision and low energy deposition. In Aim 3, I will integrate these novel methods to the task of engineering spatiotemporally trackable and controllable mammalian gut microbes. The completion of these aims will establish a platform for designing probiotics that can be monitored for their function and controlled externally by clinicians to deliver therapies at precise locations and times. Furthermore, the invention of these technologies will stimulate broad interest in other biomedical research that requires sensitive imaging and control of cellular function in deep-lying tissues. The proposal also describes research expertise training, conference attendance and the acquisition of leadership skills that, altogether, will prepare me as a competitive candidate to establish an independent research program at a major research institute and stimulate advances towards my long-term goal of developing imaging and control technologies to study intact biological systems.